VEGAWES: Variational segmentation on whole exome sequencing for copy number detection

Samreen Anjum, Sandro Morganella, Fulvio D'Angelo, Antonio Iavarone, Michele Ceccarelli

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: Copy number variations are important in the detection and progression of significant tumors and diseases. Recently, Whole Exome Sequencing is gaining popularity with copy number variations detection due to low cost and better efficiency. In this work, we developed VEGAWES for accurate and robust detection of copy number variations on WES data. VEGAWES is an extension to a variational based segmentation algorithm, VEGA: Variational estimator for genomic aberrations, which has previously outperformed several algorithms on segmenting array comparative genomic hybridization data. Results: We tested this algorithm on synthetic data and 100 Glioblastoma Multiforme primary tumor samples. The results on the real data were analyzed with segmentation obtained from Single-nucleotide polymorphism data as ground truth. We compared our results with two other segmentation algorithms and assessed the performance based on accuracy and time. Conclusions: In terms of both accuracy and time, VEGAWES provided better results on the synthetic data and tumor samples demonstrating its potential in robust detection of aberrant regions in the genome.

Original languageEnglish
Article number315
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
Publication statusPublished - 29 Sep 2015

Fingerprint

Exome
Sequencing
Segmentation
Tumors
Tumor
Synthetic Data
Neoplasms
Comparative Genomics
Comparative Genomic Hybridization
Single nucleotide Polymorphism
Glioblastoma
Nucleotides
Polymorphism
Aberrations
Aberration
Progression
Single Nucleotide Polymorphism
Genomics
Genome
Genes

Keywords

  • Copy number variation
  • Segmentation
  • Variational based model
  • Whole-exome sequencing

ASJC Scopus subject areas

  • Applied Mathematics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

VEGAWES : Variational segmentation on whole exome sequencing for copy number detection. / Anjum, Samreen; Morganella, Sandro; D'Angelo, Fulvio; Iavarone, Antonio; Ceccarelli, Michele.

In: BMC Bioinformatics, Vol. 16, No. 1, 315, 29.09.2015.

Research output: Contribution to journalArticle

Anjum, Samreen ; Morganella, Sandro ; D'Angelo, Fulvio ; Iavarone, Antonio ; Ceccarelli, Michele. / VEGAWES : Variational segmentation on whole exome sequencing for copy number detection. In: BMC Bioinformatics. 2015 ; Vol. 16, No. 1.
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